From: mdcooper (mdcooper_at_uvic.ca)
Date: Tue Oct 26 2004 - 14:31:38 CDT
Hi all,
I am running a script (see bottom) just to test a minimization/smd set up and
I am finding that during minimization the SMD seems to be running. Can anyone
tell me what is happening here?
It would not be good if the SMD was running - if that is the case, does anyone
know of an easy way to run an smd for a number of steps and then minimize. My
other option is to use the dcd output, minimize that, and then do the namd run
0 script to get energies. Does anyone see any problems with that?
Thanks,
matt
#############################################################
## EXTRA PARAMETERS ##
#############################################################
SMD on
SMDfile solvate.smd.ref
SMDk 5
SMDvel 0.0001
SMDdir -0.354926751 0.551232598 -0.013994273
SMDOutputFreq 20
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
set x 1
while {$x<10} {
minimize 100
reinitvels $temperature
run 100 ;
incr x 1
}
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:56 CST